Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function

Thomas F Clarke,Patricia L Clark

doi:10.1186/1471-2164-11-118

Abstract

BackgroundThe process of translation can be affected by the use of rare versus common codons within the mRNA transcript.ResultsHere, we show that rare codons are enriched at the 5' and 3' termini of genes from E. coli and other prokaryotes. Genes predicted to be secreted show significant enrichment in 5' rare codon clusters, but not 3' rare codon clusters. Surprisingly, no correlation between 5' mRNA structure and rare codon usage was observed.ConclusionsPotential functional roles for the enrichment of rare codons at terminal positions are explored.

Highlights

The process of translation can be affected by the use of rare versus common codons within the mRNA transcript
To quantify the relative rareness of codons used across an entire ORFeome, we used the previously developed %MinMax algorithm [6,15]. %MinMax determines the relative commonness or rareness of an mRNA sequence, given the constraints of the underlying protein sequence and the relative abundances of the codons in a particular organism
In contrast to %MinMax, other methods to quantify codon usage have focused on the relative commonness of codons [16], which is useful for estimating expression levels but is not designed for investigating the presence of rare codons or translation rate

Summary

Introduction

The process of translation can be affected by the use of rare versus common codons within the mRNA transcript. Results: Here, we show that rare codons are enriched at the 5’ and 3’ termini of genes from E. coli and other prokaryotes. No correlation between 5’ mRNA structure and rare codon usage was observed. The amino acid sequence of a protein is determined by the sequence of trinucleotide codons in its mRNA. The 20 most common amino acids are encoded by 61 different codons. With the exception of methionine and tryptophan, all of these amino acids are encoded by multiple codons, meaning that many different nucleotide sequences can encode an identical protein sequence. The higher demand for these common codons correlates with an increased production of their cognate tRNAs, leading to faster [1,2,3] and more accurate [4,5] translation of common codons relative to their rare counterparts

Methods

Results

Conclusion